Significance Simian immunodeficiency virus (SIV) infection of newborn rhesus macaques is a useful animal model of human pediatric HIV infection to investigate novel intervention strategies. PMPA has been shown to be highly effective in protecting newborn macaques against oral infection with wildtype SIVmac. It is unknown if PMPA can still protect against infection with PMPA-resistant SIV. Objectives We determined whether a 4 week PMPA dosage regimen, starting 24 h before oral virus inoculation, was able to protect newborn macaques against infection with PMPA-resistant SIVmac055. Results While untreated control animals became persistently infected, about half of the PMPA-treated animals were protected against infection with PMPA-resistant SIVmac055 by the 1-month PMPA treatment regimen. The other infants which received PMPA, became infected but had a delayed disease course. Conclusion Prophylactic PMPA administration offers partial protection against PMPA-resistant SIV. These results are important for human clinical settings where PMPA is given to reduce mother-to-infant HIV transmission, and where the mother may harbor PMPA-resistant HIV variants. KEYWORDS PMPA, vertical transmission, primate, prophylaxis, prevention, pediatrics, drug resistance